|
6
|
1 #!/usr/bin/python
|
|
|
2
|
|
|
3 import os
|
|
|
4 import shutil
|
|
|
5
|
|
|
6 # Internal dependencies
|
|
|
7 from Datatype import Datatype
|
|
|
8 from Track import Track
|
|
|
9 from TrackDb import TrackDb
|
|
|
10
|
|
|
11
|
|
|
12 class BigWig( Datatype ):
|
|
|
13 def __init__(self, input_bigwig_path, data_bigwig):
|
|
|
14 super(BigWig, self).__init__()
|
|
|
15
|
|
|
16 self.track = None
|
|
|
17
|
|
|
18 self.input_bigwig_path = input_bigwig_path
|
|
|
19 self.name_bigwig = data_bigwig["name"]
|
|
|
20 self.priority = data_bigwig["order_index"]
|
|
|
21 self.track_color = data_bigwig["track_color"]
|
|
|
22 # TODO: Think about how to avoid repetition of the group_name everywhere
|
|
|
23 self.group_name = data_bigwig["group_name"]
|
|
|
24
|
|
|
25 #print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig )
|
|
|
26
|
|
|
27 trackName = "".join( ( self.name_bigwig, ".bigwig" ) )
|
|
|
28
|
|
|
29 myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName)
|
|
|
30 shutil.copy(self.input_bigwig_path, myBigWigFilePath)
|
|
|
31
|
|
|
32 # Create the Track Object
|
|
|
33 self.createTrack(file_path=trackName,
|
|
|
34 track_name=trackName,
|
|
|
35 long_label=self.name_bigwig,
|
|
|
36 track_type='bigWig', visibility='full',
|
|
|
37 priority=self.priority,
|
|
|
38 track_file=myBigWigFilePath,
|
|
|
39 track_color=self.track_color,
|
|
|
40 group_name=self.group_name)
|
|
|
41
|
|
|
42 # dataURL = "tracks/%s" % trackName
|
|
|
43 #
|
|
|
44 # # Return the BigBed track
|
|
|
45 #
|
|
|
46 # trackDb = TrackDb(
|
|
|
47 # trackName=trackName,
|
|
|
48 # longLabel=self.name_bigwig,
|
|
|
49 # shortLabel=self.getShortName( self.name_bigwig ),
|
|
|
50 # trackDataURL=dataURL,
|
|
|
51 # trackType='bigWig',
|
|
|
52 # visibility='full',
|
|
|
53 # priority=self.priority,
|
|
|
54 # )
|
|
|
55 #
|
|
|
56 # self.track = Track(
|
|
|
57 # trackFile=myBigWigFilePath,
|
|
|
58 # trackDb=trackDb,
|
|
|
59 # )
|
|
|
60
|
|
|
61 print("- BigWig %s created" % self.name_bigwig)
|
|
|
62 #print("- %s created in %s" % (trackName, myBigWigFilePath))
|
